I'm against compiled stuff going into version control, specially when it comes to compiled binaries, however, my principles are now in question after adding doxygen support for a project.

Should the hundreds of files generated by doxygen go into version control?, what is the recommended practice here?, I think the ideal would be automating the process in a server that publishes that documentation at the same time, however, there is no such server now nor there will be for some time.

Ask yourself: What value does it add, and what does it cost? In general, it clutters repo history forever, and builds (including the documentation) should be reproducable by a single command anyway, so there ought to be little value. Plus, you can host the documentation on a shared network drive or something.
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delnanNov 13 '12 at 21:37